Paratuberculosis caused by Mycobacterium avium subsp. paratuberculosis (Map) is a progressive, chronic and non-curable granulomatous enteritis. Paratuberculosis affects ruminants worldwide. The earliest reports on paratuberculosis in Iran date back to 1960’s when the disease was diagnosed in imported animals of the Abadan Oil Company’s farm. In the work presented here 13 field MAP isolates including 4 ovine and 3 caprine isolates from Isfahan, 6 bovine isolates from Zanjan and Alborz provinces plus 2 vaccinal strains of 316F and III & V were subjected to PCR-IS900, PCR-F57 for identification and also PCR-Collins for typing. In consequence, while an identical PCR protocol was successfully developed to simultaneously perform all the three experiments, the 15 tested bacteria were all shown to be MAP Type II (cattle type). In epidemiological sense, when the size of national goat, sheep and cattle herds of Iran is taken into account, circulation of MAP Type II is intriguing.